#use strict;   ....     I think the gaps are where there are entries missing from the files...

And once again, we're back to Re^5: Combining 3 files

I also want to output the data on one line tab-delimited

So go ahead and print tabs instead of newlines, whats the problem?

Maybe you should spend a few days with perlintro or http://learn.perl.org/books/beginning-perl/